22-23895034-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_002415.2(MIF):c.282-6C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,545,856 control chromosomes in the GnomAD database, including 24,770 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_002415.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIF | NM_002415.2 | c.282-6C>G | splice_region_variant, intron_variant | ENST00000215754.8 | NP_002406.1 | |||
MIF-AS1 | NR_038911.1 | n.868G>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIF | ENST00000215754.8 | c.282-6C>G | splice_region_variant, intron_variant | 1 | NM_002415.2 | ENSP00000215754.7 | ||||
ENSG00000251357 | ENST00000433835.3 | c.605-6C>G | splice_region_variant, intron_variant | 5 | ENSP00000400325.3 |
Frequencies
GnomAD3 genomes AF: 0.175 AC: 26601AN: 152042Hom.: 2458 Cov.: 33
GnomAD3 exomes AF: 0.194 AC: 30212AN: 155428Hom.: 3222 AF XY: 0.192 AC XY: 15817AN XY: 82308
GnomAD4 exome AF: 0.176 AC: 245858AN: 1393700Hom.: 22307 Cov.: 35 AF XY: 0.177 AC XY: 121390AN XY: 686648
GnomAD4 genome AF: 0.175 AC: 26628AN: 152156Hom.: 2463 Cov.: 33 AF XY: 0.180 AC XY: 13400AN XY: 74370
ClinVar
Submissions by phenotype
MIF-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at